GNOM Global X Genomics and Biotechnology

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 14D-9

(Amendment No. 12)

Solicitation/Recommendation Statement

under Section 14(d)(4) of the Securities Exchange Act of 1934

Complete Genomics, Inc.

(Name of Subject Company)

Complete Genomics, Inc.

(Names of Person(s) Filing Statement)

Common Stock, $0.001 par value per share

(Title of Class of Securities)

20454K104

(CUSIP Number of Class of Securities)

A. W. Homan

Senior Vice President, General Counsel and Secretary

Complete Genomics, Inc.

2071 Stierlin Court

Mountain View, California 94043

(650) 943-2800

(Name, address and telephone numbers of person authorized to receive

notices and communications on behalf of the persons filing statement)

with copies to:

Alan C. Mendelson

Latham & Watkins LLP

140 Scott Drive

Menlo Park, CA 94025

(650) 328-4600

This Amendment No. 12 (the “ Amendment ”) amends and supplements the Solicitation/Recommendation Statement on Schedule 14D-9 of Complete Genomics, Inc. (“ Complete ” or the “ Company ”) filed with the Securities and Exchange Commission (the “ SEC ”) on September 25, 2012 and amended on September 27, 2012, October 2, 2012, October 5, 2012, October 22, 2012, November 2, 2012, November 13, 2012, November 15, 2012, November 20, 2012, November 26, 2012, November 27, 2012 and November 28, 2012 (as amended, the “ Schedule 14D-9 ”). The Schedule 14D-9 relates to the tender offer by Beta Acquisition Corporation, a Delaware corporation (“ Purchaser ”) and a wholly owned subsidiary of BGI-Shenzhen, a company organized under the laws of the People’s Republic of China (“ Parent ” or “ BGI ”), to purchase all of the outstanding common stock, par value $0.001 per share, of Complete (the “ Shares ”), at a price of $3.15 per Share, net to seller in cash, without interest and less any applicable withholding taxes, upon the terms and conditions set forth in the Offer to Purchase dated September 25, 2012 (the “ Offer to Purchase ”) and the related Letter of Transmittal (which, together with the Offer to Purchase, as each may be amended or supplemented from time to time, constitute the “ Offer ”). The Offer is described in a Tender Offer Statement on Schedule TO filed by Parent and Purchaser with the SEC on September 25, 2012. The Offer to Purchase and the Letter of Transmittal were filed with the Schedule 14D-9 as Exhibits (a)(1)(A) and (a)(1)(B), respectively.

Except as otherwise set forth below, the information set forth in the Schedule 14D-9 remains unchanged and is incorporated by reference as relevant to the items in this Amendment. Capitalized terms used and not defined herein shall have the meanings assigned to such terms in the Schedule 14D-9. This Amendment is being filed to reflect certain updates as reflected below.

Item 8.   Additional Information.

Item 8 of the Schedule 14D-9 is hereby amended and supplemented to replace the final two paragraphs of the Section entitled “Subsequent Events” in their entirety with the following:

On November 27, 2012, the Court of Chancery preliminarily enjoined, until a trial on the merits, a provision in the confidentiality agreement with Party J the terms of which prohibit Party J from privately approaching the Company Board to request permission to, among other matters, make a proposal to acquire the Company. This action was not taken by the Court in response to any communication, request or proposal from Party J or representative or agent of Party J.

On November 27, 2012, the Company provided written notice to Party J of the Court of Chancery’s ruling and that the Company would interpret the confidentiality agreement with Party J as only prohibiting Party J from publicly requesting permission to, among other matters, make a proposal to acquire the Company. Party J has not communicated with the Company or made any request or proposal to the Company in response to this written notice, or otherwise since August 2, 2012, as detailed above.

2

SIGNATURE

After due inquiry and to the best of my knowledge and belief, I certify that the information set forth in this Statement is true, complete and correct.

Dated: December 7, 2012

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